Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/CombineTags.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python
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2 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 # Copyright INRA-URGI 2009-2011
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4 #
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5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 import os
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32 import random
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33 from optparse import OptionParser
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34 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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35 from SMART.Java.Python.misc.Progress import Progress
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36 from commons.core.parsing.ParserChooser import ParserChooser
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37 from commons.core.writer.Gff3Writer import Gff3Writer
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38
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39 OPERATIONS = ("plus", "minus", "times", "div")
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40
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41 class CombineTags(object):
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42
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43 def __init__(self, verbosity = 0):
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44 self.verbosity = verbosity
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45
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46 def setInputFile(self, fileName, format):
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47 self.inputFileName = fileName
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48 parserChooser = ParserChooser(self.verbosity)
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49 parserChooser.findFormat(format, "transcript")
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50 self.parser = parserChooser.getParser(fileName)
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51
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52 def setOutputFile(self, fileName):
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53 self.outputWriter = Gff3Writer(fileName, self.verbosity)
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54
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55 def setTags(self, tag1, tag2, outputTag, defaultValue = None):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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56 self.tag1 = tag1
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57 self.tag2 = tag2
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58 self.outputTag = outputTag
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59 self.defaultValue = defaultValue
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60
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61 def setOperation(self, operation):
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62 self.operation = operation
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63 if self.operation not in OPERATIONS:
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64 raise Exception("Do no handle operation %s, only: %s" % (self.operation, ", ".join(OPERATIONS)))
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65
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66 def run(self):
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67 progress = Progress(self.parser.getNbTranscripts(), "Printing transcripts %s" % (self.inputFileName), self.verbosity)
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68 for transcript in self.parser.getIterator():
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69 tag1 = transcript.getTagValue(self.tag1)
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70 tag2 = transcript.getTagValue(self.tag2)
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71 if tag1 == None or tag2 == None:
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72 if self.defaultValue == None:
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73 raise Exception("Transcript %s misses one of the tags %s and %s, and has no default value !" % (transcript, self.tag1, self.tag2))
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74 newTag = self.defaultValue
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75 else:
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76 tag1, tag2 = float(tag1), float(tag2)
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77 if self.operation == "plus":
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78 newTag = tag1 + tag2
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79 elif self.operation == "minus":
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80 newTag = tag1 - tag2
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81 elif self.operation == "times":
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82 newTag = tag1 * tag2
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83 elif self.operation == "div":
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84 newTag = tag1 / tag2
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85 transcript.setTagValue(self.outputTag, newTag)
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86 self.outputWriter.addTranscript(transcript)
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87 progress.inc()
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88 progress.done()
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89 self.parser.close()
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90 self.outputWriter.close()
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91
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92
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93 if __name__ == "__main__":
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94
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95 # parse command line
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96 description = "Change Tag Name v1.0.1: Change the name of tag of a list of transcripts. [Category: Data Modification]"
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97
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98 parser = OptionParser(description = description)
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99 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
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100 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
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101 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
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102 parser.add_option("-t", "--tag1", dest="tag1", action="store", type="string", help="name of the first tag [compulsory] [format: string]")
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103 parser.add_option("-T", "--tag2", dest="tag2", action="store", type="string", help="name of the second tag [compulsory] [format: string]")
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104 parser.add_option("-d", "--default", dest="defaultValue", action="store", default=None, type="string", help="default value when one of the tag is absent [compulsory] [format: float]")
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105 parser.add_option("-n", "--new", dest="newTag", action="store", type="string", help="name of the new tag [compulsory] [format: string]")
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106 parser.add_option("-p", "--operation", dest="operation", action="store", type="string", help="operation combining the tags [compulsory] [format: choice (plus, minus, times, div)]")
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107 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")
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108 (options, args) = parser.parse_args()
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109
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110 combiner = CombineTags(options.verbosity)
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111 combiner.setInputFile(options.inputFileName, options.inputFormat)
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112 combiner.setOutputFile("%s.gff3" % (options.outputFileName))
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113 combiner.setTags(options.tag1, options.tag2, options.newTag, options.defaultValue)
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114 combiner.setOperation(options.operation)
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115 combiner.run()